Look, while I agree that the story of Naruto started getting a little sloppy and missed the mark entirely of what made the series so great in the first place, you likewise missed the mark entirely of the process of making a manga. My intention here is not to come off as rude, but if you wish to become a mangaka like you claim then there are some fundamental principles you need to understand.
First off, Kishimoto did in fact have advisors when he started the manga. The character of Sasuke was not originally created until Kishimoto's advisory board suggested that he added a rival character to butt heads with the main hero. That proves that there used to be a system in place, as any starting mangaka should have. Heres where the system starts to fall apart, much akin to George Lucas with Star Wars. Once a creator achieves a certain level of success either A. that creator no longer believes they need a support system, B. the support system no longer deems it necessary as the success of the content speaks for itself, or C. the storyteller receives advise but has already developed the story in a certain direction and is set on that motion. The consumers will eat anything at that point, thus there is not a high demand for quality work, so much as there is product to be consumed. I would assume at this point Kishimoto no longer has advisors to steer the story a certain direction, as it has been over 10 long years of success. He has proven that he can handle the material, at least to his support system.
Second, the fan base. Fans and critics are crucial for progressing any work. Especially art. However, when telling a story things get a little different. Now, I will not go off explaining the fundamentals of storytelling as that is an entirely different ball park, but I will summarize it up with this: As a storyteller, to tell a strong story, the story must pull from an emotion or a theme that resonates with you. The core that the entire story is structured around must be powerful, or else no one else will care about it. It is up to you, the storyteller to carry out this theme and tell your own story. If Kishimoto had changed anything at all in Naruto just because his "fans" were complaining about it, then it would significantly diminish the value of the story, as from that moment on it is not his story. At that point, he is nothing more than a vehicle for the entire world to tell a story, and thus defeats the purpose of the storyteller. Fans are important, and speculation / debates amongst the fan base is equally important as it keeps the material relevant. However you must never give in to peer pressure. True fans will appreciate the material no matter what, and if your story's core is strong enough then you will never have doubts in where you take your story.